Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent

Similar Threads
Thread Thread Starter Forum Replies Last Post
Concentration of mismatches close to read ends in "Whole Transcriptome" protocol hingamp SOLiD 42 05-27-2010 04:43 AM
watch out, biases! mudshark Epigenetics 1 08-28-2009 09:45 AM
GS Mapper output to consed shows dimmed ends with good sequence? gaster 454 Pyrosequencing 0 05-11-2009 12:43 PM
Paper: Substantial biases in ultra-short read data sets from HTP DNA sequencing ECO Illumina/Solexa 0 08-02-2008 05:16 PM
PubMed: Substantial biases in ultra-short read data sets from high-throughput DNA seq Newsbot! Literature Watch 0 07-29-2008 05:10 AM

Thread Tools
Old 11-22-2011, 03:46 AM   #1
Senior Member
Location: uk

Join Date: Jan 2010
Posts: 110
Default Sequence biases toward read ends

I'm just having a look at the publicly available DH10B data with the FastQC program and notice some pretty huge spikes in sequence bias at the 3' end, with smaller rises at the 5` end. Being new to Ion Torrent data I'm wondering if anyone can explain what I am seeing?

Thanks in advance.

Last edited by gavin.oliver; 11-22-2011 at 04:00 AM.
gavin.oliver is offline   Reply With Quote
Old 11-23-2011, 07:50 AM   #2

Posts: n/a

Do you mean slopes or spikes? Keep in mind the x axis is not linear with FastQC, so it tends to misrepresent 3' quality in PGM data. I think a few blogs have mentioned this.

I still use FastQC for a quick look at quality, but it's built around Illumina error models.
  Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:39 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO